Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem
On 5/18/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > shahid nayeem wrote: > >> Dear All >> I downloaded dsspcmbi.tar.gz, and compiled using command >> ./DsspCompileGCC as given in Readme.txt file. when I try to run >> do_dssp command in gromacs I get error >> > > Well, what happened? > > >> Fatal error: >> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) >> >> I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I >> > > It won't be there unless you put it there and you have re-named it. I > believe the default name of the dssp program is "dsspcmbi," which you need > to change when you move the executable. > > http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp > > -Justin > > even tried dsspcmbi.zip file but again I got the same error. I >> compiled dssp as root. Now what shoul I do in order to run do_dssp >> comand of gromacs. >> Shahid nayeem >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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